==== MRC Headers ====

**Headers of the MRC programs, but in the 2DX modified version. Please use these as *rough* guidelines, but check in the actual programs for the current state of your local copy.**


[[Padbox|Padbox]]
Adds data around the edge.


[[ttboxk|Ttboxk]]
Prints out amplitudes & phases in N * N boxes from a Fourier transform, fully corrected for contrast transfer function in tilted image.

[[mmboxa|Mmboxa]]
Derived from Judy Smith's NNBOX program but with more statistics suitable for more high resolution crystallographic analysis.

[[twolat|Twolat]]
Plots two lattices to see if there is an overlap.

[[label|Label]]
Program to perform simple manipulations on image files

[[Fftrans|Fftrans]]
FFT

[[pickprofk|Pickprofk]]
Program for electron diffraction spots integration, using least-squares profile-fitting.

[[ttrefine|Ttrefine]]
Refines defocus, astigmatism, tiltaxis and tiltangle in images of thin tilted crystals.

[[latline|Latline]]
This is a program to do fitting of curves to either Intensity or F,Phi data for individual layer lines.

[[ttmask|Ttmask]]
Program for masking a Fourier transform, with simultaneous correction for tilted contrast transfer function.

[[avrgamphs|Avrgamphs]]
Program to obtain weighted average phases from merged list.

[[boximage|Boximage]]
Simple boxing program to create circular or polygonal box with no change in image size.

[[ctfapplyk|Ctfapplyk]]
Derived from CTFPLOT giving automatic application of CTF to phases input from MMBOX and output ready for ORIGTILT. Program plots spots from MMBOX in reciprocal space and CTF plot of image.

[[ctftilt|Ctftilt]]
Program determines defocus, astigmatism tilt axis and tilt angle for images of arbitrary size (MRC format). Astigmatic angle is measured from x axis (same conventions as in the MRC 2D image processing programs).

[[allspace|Allspace]]
Umbrella program to calculate internal phase residual in all 17 space groups from data on a single film. Can do the same thing within one film as ORIGTILT does between different films.

[[convdeconv|Convdeconv]]
Program to read in a list of amplitudes and phases and calculate a new list of amplitudes and phases which represent either the convolution or deconvolution of the original.

[[quadserck|Quadserchk]]
Cross-correlation searching program.

[[ctffind2|Ctffind2]]
Determines defocus and astigmatism for images of arbitrary size (MRC format). Astigmatic angle is measured form x axis (same convetiones as in the MRC 2D image processing programs).

[[rfiltim|Rfiltim]]
Rotational filtering of images in reciprocal space.

[[syncfitp3|Syncfitp3]]
Fits SYNC functions to lattice lines produced by MERGHIGH with or without preparation of input data set for plotting version. Includes estimates of errors in SYNC function coeffs and errors in fitted curve.

[[maketran|Maketran]]
This program reads in a MTZ file of diffraction amplitudes and phases from the experimentally determined and merged 3-D data from a 2-dimensional crystal, and writes out the transform of the projection of the structure in the direction, at the magnification, and modified by the requested CTF for later use as a reference in cross-correlation with the digitized experimental image.

[[mmlatref|Mmlatref]]
Refinement of lattice parameters for maximum amplitude.

[[pickauto|Pickauto]]
Program to integrate spots on a lattice.

[[backauto|Backauto]]
Program to calculate the mean radial density (background) of an electron diffraction pattern - any size rectangular area. The new version has options to carry out automatic center determination, and update of the header into the invisible IEXTRA records used by the subsequent program PICKYCOR.

[[taperedge|Taperedge]]
Simple program to taper edges of a rectangular image so that there are no sharp discontinuities which make the Fourier transform contain spikes.

[[twofile|Twofile]]
Program to perform simple additions or multiplications on 2 images of same dimensions and type (i.e. both must be real or both complex).

[[latlineprescal|Latlineprescal]]
Program to correct image amplitudes for effects of CTF and to calculate appropriate weights for output to LATLINE.

[[origtiltk|Origtiltk]]
Three-dimensional origin, beam tilt and crystal tilt refinement.

[[ttboxref|Ttboxref]]
Refines lattice parameters in image transform of tilted specimen.

[[ctffind|Ctffind]]
This program will attempt to determine the defocus (not yet astigmatism) of any general image whether or not it contains crystalline areas. The program will also apply a CTF correction either by multiplication or division (accompanied by a Wiener filter). Both amplitude and phase contrast with astigmatism can be applied.

[[masktran|Masktran]]
Program for masking a Fourier transform.

[[scalimamp3d|Scalimamp3d]]
Program to scale up image amplitudes to restore the resolution-dependent fall off due to image blurring, radiation damage, temperature factor, static disorder, charging or any other source of power loss.

[[ccunbendk|Ccunbendk]]
Program unbends the crystal using output from the cross-correlation peak search program, CCORSERCH or its later variants PROFSERCH and QUADSERCH (0, 1, and 2).